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A Promising Target to Limit the Local Invasiveness of Colorectal Cancer

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A Promising Target to Limit the Local Invasiveness of Colorectal Cancer Supplementary Materials Aspartate-β-Hydroxylase: A Promising Target to Limit the Local Invasiveness of Colorectal Cancer Roberto Benelli, Delfina Costa, Luca Mastracci, Federica Grillo, Mark Jon Olsen, Paola Barboro, Alessandro Poggi and Nicoletta Ferrari Figure S1. ASPH mRNA levels in the normal tissue (blue) and the related cancer (red) of all available TCGA samples (analysis by UALCAN website). Samples with a highly statistically significant increase of ASPH mRNA levels in tumor tissue (p < 0.0001) are highlighted in bold in the list below. The number of normal and tumor samples available for comparison is indicated (vs = versus). BLCA bladder urothelial carcinoma, 19 vs 408 BRCA breast invasive carcinoma, 114 vs 1097 CESC cervical squamous cell carcinoma, 3 vs 305 CHOL cholangiocarcinoma, 9 vs 36 COAD colon adenocarcinoma, 41 vs 286 ESCA esophageal carcinoma, 11 vs 184 GBM glioblastoma multiforme, 5 vs 156 HNSC head and neck squamous cell carcinoma, 44 vs 520 KICH kidney chromofobe, 25 vs 67 KIRC kidney clear cell carcinoma, 72 vs 533 KIRP kidney papillary cell carcinoma, 32 vs 290 LIHC liver hepatocellular carcinoma, 50 vs 371 LUAD lung adenocarcinoma, 59 vs 515 LUSC lung squamous cell carcinoma, 52 vs 503 PAAD pancreatic adenocarcinoma, 4 vs 178 PRAD prostate adenocarcinoma, 52 vs 497 PCPG pheochromocytoma and paraganglioma, 3 vs 179 READ rectal adenocarcinoma, 10 vs 166 SARC sarcoma, 2 vs 260 SKCM skin cutaneous melanoma, 1 vs 472 THCA thyroid carcinoma, 59 vs 505 THYM thymoma, 2 vs 120 STAD stomach adenocarcinoma, 34 vs 415 UCEC uterine corpus endometrial carcinoma, 35 vs 546 Figure S2. Comparison of the methylation status of each region of ASPH gene in CRC and normal colon mucosa. The analysis shows that ASPH gene promoter is not the only target of a differential methylation. Methylation involves also single CpG dinucleotides probably regulating alternative splicing. CRC and normal mucosa share the same sites of methylation (p reported on the right for each putative site of methylation). Analysis performed by MEXPRESS (https://mexpress.be). Figure S3. Analysis of chromosomal regions identifying clusters of genes potentially co-amplified with ASPH in human cancers. Analysis performed by the Broad Institute web platform (http://portals.broadinstitute.org/tcga). Please find below the list of the 115 amplified genes clustering with ASPH in the peak region, in CRC. In the red square is highlighted the small cluster of 8 genes co-amplified in lung cancer. Figure S4. ASPH antibody characterization: (a) Western blot analysis of ASPH expression in lysates from CRC cell lines (whole blot for both ASPH and beta-actin proteins is shown); (b)Western blot analysis of ASPH expression in tissue samples (whole blot is shown for ASPH protein). N, normal tissue; T, tumor tissue. Long exposures reveal a unique band corresponding to the active high molecular weight form (86kDa) of ASPH. (c) Whole blot of beta actin and table with desitometric values of ASPH, and their ratio with β-actin, reported in order of appearance; (d) Full size images of blots shown in figure 4 and their densitometric quantification. Quantifications are shown in order of appearance. Figure S5. Example of digital pathology analysis of the luminal area (LM), central tumor (CT) and invasive margin (IM) of a CRC specimen, stained by anti ASPH antibody. Annotated regions of interest (ROI) are shown in pink squares. The recognition of tumor cells and the resultant H-score quantification of ASPH was obtained combining a trained Genie algorithm with a modified Cytoplasmic v2 macro of the Image Scope software. Scale bar: 200 µm. Figure S6. Examples of CRC samples with null/low (left), or high (right) ASPH expression. Scale bar: 300 µm. Figure S7. Normal and hyperplastic mucosa is negative, or faintly stained for ASPH, as compared to the adjacent CRC. Red scale bar: 400 µm; yellow scale bar: 200 µm. Figure S8. Analysis of ASPH levels in CRC samples with microsatellite instability (MSI): (a) analysis of ASPH mRNA levels in 434 TCGA-COAD CRC samples compared to MSI, APC mutation (surrogate marker for chromosomal instability, CIN) and CIMP (CpG island methylator phenotype); (b) A close-up of 133 samples with MSS/MSI available data (ASPH mRNA levels were available for 11 MSI samples); (c) Comparison of ASPH protein levels (H-Scores) in the IM, CT and LM of our samples using available data on microsatellite status (15 MSI, 72 MSS, excluded 13 not classified). The analyses shown in panels a and b were obtained using Xena functional genomics explorer (https://xenabrowser.net). Figure S9. Kaplan-Meier analysis of overall survival in TCGA-COAD patients according to low or high ASPH mRNA levels (the median of data was used as cut-off threshold). p = 0.735. Figure S10. Screening of SMIs on ASPH catalytic activity in CRC cell lines SW480 and DLD1. A panel of ASPH inhibitors was screened to select active compounds and optimize concentrations for further analysis. Graphed data compare the effects of MO-I-1100, MO-I-1151, MO-I-1182, MO-I-1144, MO-I-1150 and MO-I- 1187 at concentrations ranging from 1 to 30µM. Dose-effects of the SMIs on cell viability were measured relative to vehicle-treated control cells using the crystal violet or the invasion test. MO-I-1144 compound resulted the only effective although at high concentrations. Figure S11: Structures of ASPH SMIs. Table S1: Evaluation of Immune, NOTCH and Invasive mRNA signatures, according to ASPH levels, in COAD (Firehouse legacy) TCGA samples. Pearson’s correlation r indexes with significant p values are color- graded according to the following scale: red r > 0.2, orange 0 < r<0.2, green -0.2 < r<0, blue r < -0.2. Significant Q values are reported in bold. Immune signature ASPH vs Pearson r 95% CI p Q CD3G 0.0509 -0.0814 0.181 0.451 0.414 CD8B -0.108 -0.236 0.0242 0.109 0.157 CD4 -0.0321 -0.163 0.100 0.634 0.524 PTPRC-CD45 0.0802 -0.052 0.210 0.234 0.265 CD68 0.034 -0.0981 0.165 0.614 0.515 NCR1-NKp44 0.178 0.0474 0.303 0.00786 0.034 NCR2-NKp46 -0.120 -0.248 0.0115 0.0735 0.114 CTLA4 0.127 -0.00477 0.254 0.0589 0.106 PDCD1-PD1 0.141 0.00945 0.268 0.0358 0.083 CD274-PDL1 0.307 0.183 0.422 3.16e-06 9.14e-05 Notch signature ASPH vs Pearson r 95% CI p Q ADAM10 0.123 -0.0148 0.257 0.08 0.121 ADAM17 0.075 -0.0634 0.21 0.288 0.297 APH1A 0.152 0.015 0.284 0.03 0.082 APH1B -0.0962 -0.231 0.0421 0.172 0.216 ARRDC1 0.021 -0.117 0.158 0.767 0.573 CTBP1 0.0986 -0.0397 0.233 0.162 0.213 CTBP2 -0.045 -0.182 0.0933 0.524 0.466 CUL1 0.0157 -0.122 0.153 0.824 0.574 DLL1 -0.043 -0.18 0.0953 0.543 0.469 DLL3 -0.108 -0.242 0.0299 0.124 0.175 DLL4 -0.0192 -0.156 0.119 0.786 0.574 DTX1 0.0116 -0.126 0.149 0.87 0.592 DTX2 -0.0863 -0.221 0.0521 0.221 0.259 DTX3 -0.169 -0.299 -0.0316 0.0162 0.054 DTX3L 0.142 0.00451 0.274 0.0431 0.089 DTX4 0.00238 -0.135 0.14 0.973 0.625 EP300 -0.105 -0.239 0.0333 0.137 0.188 FBXW7 -0.0396 -0.176 0.0987 0.575 0.489 HDAC1 0.0162 -0.122 0.154 0.818 0.574 HDAC2 -0.147 -0.279 -0.00914 0.0368 0.083 HES1 -0.0969 -0.231 0.0414 0.169 0.216 HEYL -0.126 -0.259 0.0117 0.0727 0.114 ITCH -0.181 -0.311 -0.0446 0.00966 0.039 JAG1 0.0438 -0.0945 0.18 0.535 0.469 JAG2 0.0813 -0.057 0.217 0.249 0.277 LFNG -0.304 -0.424 -0.173 1.06e-05 0.0002 MAML1 0.0298 -0.108 0.167 0.673 0.540 MAML2 0.129 -0.00844 0.262 0.0657 0.108 MAML3 0.0662 -0.0722 0.202 0.348 0.341 MFNG 0.055 -0.0834 0.191 0.436 0.406 NCOR2 0.0286 -0.11 0.166 0.686 0.543 NCSTN -0.146 -0.278 -0.00868 0.0374 0.083 NOTCH1 -0.0925 -0.227 0.0458 0.19 0.230 NOTCH2 0.167 0.0302 0.298 0.0171 0.054 NOTCH3 -0.0677 -0.203 0.0707 0.337 0.339 NOTCH4 -0.0041 -0.142 0.134 0.954 0.620 NUMB 0.240 0.106 0.366 0.000565 0.005 NUMBL 0.122 -0.0158 0.256 0.0825 0.122 PSEN1 0.214 0.0789 0.342 0.00214 0.015 PSEN2 -0.129 -0.262 0.00844 0.0657 0.108 PSENEN 0.0237 -0.114 0.161 0.737 0.573 RBPJ 0.269 0.137 0.392 0.000102 0.001 RBPJL -0.169 -0.3 -0.0323 0.0158 0.054 RFNG 0.179 0.0418 0.309 0.0108 0.041 SNW1 0.330 0.201 0.447 1.53e-06 8.85e-05 SPEN 0.130 -0.00833 0.263 0.065 0.108 HES2 -0.00536 -0.143 0.132 0.94 0.618 HES4 0.137 -0.000606 0.27 0.0511 0.098 HES7 0.0067 -0.131 0.144 0.924 0.614 HEY1 -0.012 -0.149 0.126 0.865 0.592 HEY2 -0.0798 -0.215 0.0585 0.257 0.277 Invasive signature ASPH vs Pearson r 95% CI p Q MMP1 0.190 0.0539 0.32 0.00656 0.031 MMP2 0.0549 -0.0834 0.191 0.436 0.406 MMP3 0.150 0.0122 0.282 0.0331 0.083 MMP7 0.0617 -0.0766 0.198 0.382 0.368 MMP9 0.0203 -0.118 0.158 0.773 0.573 MMP10 -0.0168 -0.154 0.121 0.81 0.574 MMP11 -0.229 -0.355 -0.0939 0.00103 0.008 MMP12 0.0922 -0.0461 0.227 0.191 0.230 MMP13 0.162 0.0248 0.293 0.0209 0.061 MMP14 0.208 0.0719 0.336 0.00296 0.015 MMP15 -0.0486 -0.185 0.0898 0.492 0.444 MMP16 -0.000744 -0.138 0.137 0.992 0.630 MMP17 -0.0216 -0.159 0.116 0.759 0.573 MMP19 -0.0315 -0.168 0.107 0.656 0.534 MMP21 -0.0772 -0.213 0.0611 0.273 0.287 MMP23B -0.162 -0.293 -0.0247 0.0211 0.061 MMP24 -0.149 -0.281 -0.0115 0.0339 0.083 MMP25 0.0992 -0.0391 0.234 0.159 0.213 MMP26 -0.0857 -0.221 0.0527 0.224 0.259 MMP27 0.010 -0.128 0.148 0.887 0.596 MMP28 0.134 -0.00366 0.267 0.0564 0.105 ITGB3 0.0673 -0.0711 0.203 0.34 0.339 ITGAV 0.144 0.00673 0.277 0.04 0.085 PTK2 0.291 0.16 0.413 2.45e-05 0.0003 CDH1 -0.212 -0.34 -0.0762 0.00243 0.015 CDH2 -0.0215 -0.153 0.11 0.75 0.573 SPARC 0.0174 -0.121 0.155 0.805 0.574 WFDC2 -0.0796 -0.215 0.0588 0.259 0.277 TIMP1 0.138 0.000221 0.27 0.0497 0.098 TIMP2 0.209 0.0732 0.337 0.00279 0.015 Table S2.
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